# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 00:02:13 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 2-[4-[(4-cyclopropyl-1,2,3-triazol-1-yl)methyl]-2-oxidanyl-phenoxy]benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(Cn2cc(nn2)C3CC3)ccc1Oc4ccccc4C#N
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 XTV  XTV  2-[4-[(4-cyclopropyl-1,2,3-triazol-1-yl)methyl]-2-oxidanyl-phenoxy]benzenecarbonitrile  ligand  41  25  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XTV
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 XTV  NAA  N  NS    0  -0.248   6.1819  -1.0410   0.0585
 XTV  CAC  C  CSP   0   0.070   5.3971  -0.1975   0.0793
 XTV  CAT  C  CR6   0  -0.079   4.4418   0.8577   0.1094
 XTV  CAF  C  CR16  0  -0.236   4.8565   2.1813   0.2556
 XTV  CAD  C  CR16  0  -0.263   3.9195   3.1974   0.2872
 XTV  CAE  C  CR16  0  -0.229   2.5708   2.8855   0.1684
 XTV  CAG  C  CR16  0  -0.327   2.1429   1.5737   0.0206
 XTV  CAW  C  CR6   0   0.395   3.0816   0.5537  -0.0096
 XTV  OAQ  O  O2    0  -0.512   2.7855  -0.7587  -0.1658
 XTV  CAV  C  CR6   0   0.195   1.4731  -1.1706  -0.0807
 XTV  CAR  C  CR6   0   0.326   0.8308  -1.5385  -1.2601
 XTV  CAJ  C  CR16  0  -0.394  -0.4823  -1.9978  -1.1856
 XTV  OAB  O  OH1   0  -0.616   1.4202  -1.4692  -2.4638
 XTV  CAI  C  CR16  0  -0.281   0.8321  -1.2618   1.1436
 XTV  CAH  C  CR16  0  -0.305  -0.4731  -1.7163   1.2043
 XTV  CAS  C  CR6   0   0.133  -1.1340  -2.0834   0.0342
 XTV  CAN  C  CH2   0  -0.419  -2.5601  -2.5627   0.0915
 XTV  NAY  N  NR5   0  -0.242  -3.4697  -1.4820   0.4221
 XTV  CAK  C  CR15  0  -0.098  -3.8939  -0.4869  -0.3760
 XTV  NAP  N  N     0  -0.105  -3.9277  -1.3355   1.6488
 XTV  NAO  N  N     0  -0.332  -4.6552  -0.2692   1.6741
 XTV  CAU  C  CR5   0   0.209  -4.6685   0.2960   0.4464
 XTV  CAX  C  CH1   0  -0.349  -5.4230   1.5237   0.1569
 XTV  CAL  C  CH2   0  -0.478  -6.1331   1.6848  -1.1601
 XTV  CAM  C  CH2   0  -0.479  -4.9190   2.5016  -0.8682
 XTV  H1   H  HCR6  0   0.288   5.9117   2.3990   0.3470
 XTV  H2   H  HCR6  0   0.275   4.2365   4.2241   0.4028
 XTV  H3   H  HCR6  0   0.282   1.8312   3.6745   0.1882
 XTV  H4   H  HCR6  0   0.297   1.0864   1.3625  -0.0731
 XTV  H5   H  HCR6  0   0.277  -0.9850  -2.2877  -2.1007
 XTV  H6   H  HOH1  0   0.478   2.3558  -1.2483  -2.3798
 XTV  H7   H  HCR6  0   0.287   1.3585  -0.9821   2.0477
 XTV  H8   H  HCR6  0   0.264  -0.9715  -1.7906   2.1623
 XTV  H9   H  HCH2  0   0.300  -2.8686  -2.9894  -0.8619
 XTV  H10  H  HCH2  0   0.304  -2.6885  -3.3284   0.8552
 XTV  H11  H  HCR5  0   0.307  -3.6261  -0.4175  -1.4172
 XTV  H12  H  HCH1  0   0.269  -5.9142   1.9434   1.0264
 XTV  H13  H  HCH2  0   0.255  -6.0461   0.8759  -1.8748
 XTV  H14  H  HCH2  0   0.261  -7.0981   2.1746  -1.1540
 XTV  H15  H  HCH2  0   0.261  -5.0456   3.5556  -0.6577
 XTV  H16  H  HCH2  0   0.254  -3.9986   2.2572  -1.3845

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 XTV  NAO  CAU  aromatic  1.352  0.020  1.352
 XTV  NAO  NAP  aromatic  1.291  0.020  1.291
 XTV  CAX  CAM  single    1.504  0.020  1.504
 XTV  CAX  CAU  single    1.470  0.020  1.470
 XTV  CAX  CAL  single    1.505  0.020  1.505
 XTV  CAM  CAL  single    1.492  0.020  1.492
 XTV  CAU  CAK  aromatic  1.375  0.020  1.375
 XTV  NAP  NAY  aromatic  1.318  0.020  1.318
 XTV  NAY  CAK  aromatic  1.344  0.020  1.344
 XTV  NAY  CAN  single    1.451  0.020  1.451
 XTV  CAH  CAI  aromatic  1.383  0.020  1.383
 XTV  CAH  CAS  aromatic  1.393  0.020  1.393
 XTV  CAN  CAS  single    1.506  0.020  1.506
 XTV  CAI  CAV  aromatic  1.385  0.020  1.385
 XTV  CAS  CAJ  aromatic  1.386  0.020  1.386
 XTV  CAV  OAQ  single    1.378  0.020  1.378
 XTV  CAV  CAR  aromatic  1.392  0.020  1.392
 XTV  CAG  CAE  aromatic  1.388  0.020  1.388
 XTV  CAG  CAW  aromatic  1.387  0.020  1.387
 XTV  CAJ  CAR  aromatic  1.393  0.020  1.393
 XTV  CAE  CAD  aromatic  1.389  0.020  1.389
 XTV  OAQ  CAW  single    1.354  0.020  1.354
 XTV  CAW  CAT  aromatic  1.399  0.020  1.399
 XTV  CAR  OAB  single    1.342  0.020  1.342
 XTV  CAD  CAF  aromatic  1.383  0.020  1.383
 XTV  CAT  CAF  aromatic  1.395  0.020  1.395
 XTV  CAT  CAC  single    1.424  0.020  1.424
 XTV  CAC  NAA  triple    1.152  0.020  1.152
 XTV  CAF  H1   single    0.930  0.020  1.080
 XTV  CAD  H2   single    0.930  0.020  1.080
 XTV  CAE  H3   single    0.930  0.020  1.080
 XTV  CAG  H4   single    0.930  0.020  1.080
 XTV  CAJ  H5   single    0.930  0.020  1.080
 XTV  OAB  H6   single    0.850  0.020  0.980
 XTV  CAI  H7   single    0.930  0.020  1.080
 XTV  CAH  H8   single    0.930  0.020  1.080
 XTV  CAN  H9   single    0.970  0.020  1.090
 XTV  CAN  H10  single    0.970  0.020  1.090
 XTV  CAK  H11  single    0.930  0.020  1.080
 XTV  CAX  H12  single    0.970  0.020  1.090
 XTV  CAL  H13  single    0.970  0.020  1.090
 XTV  CAL  H14  single    0.970  0.020  1.090
 XTV  CAM  H15  single    0.970  0.020  1.090
 XTV  CAM  H16  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 XTV  CAT  CAC  NAA  180.00  3.000
 XTV  CAW  CAT  CAF  120.28  3.000
 XTV  CAF  CAT  CAC  120.41  3.000
 XTV  CAW  CAT  CAC  119.31  3.000
 XTV  H1   CAF  CAD  120.76  3.000
 XTV  H1   CAF  CAT  119.34  3.000
 XTV  CAD  CAF  CAT  119.90  3.000
 XTV  H2   CAD  CAE  120.48  3.000
 XTV  H2   CAD  CAF  120.12  3.000
 XTV  CAE  CAD  CAF  119.40  3.000
 XTV  H3   CAE  CAG  118.72  3.000
 XTV  H3   CAE  CAD  119.90  3.000
 XTV  CAG  CAE  CAD  121.38  3.000
 XTV  H4   CAG  CAW  121.05  3.000
 XTV  H4   CAG  CAE  119.68  3.000
 XTV  CAW  CAG  CAE  119.27  3.000
 XTV  OAQ  CAW  CAG  124.56  3.000
 XTV  OAQ  CAW  CAT  115.66  3.000
 XTV  CAG  CAW  CAT  119.77  3.000
 XTV  CAV  OAQ  CAW  119.39  3.000
 XTV  CAI  CAV  CAR  121.19  3.000
 XTV  CAR  CAV  OAQ  117.78  3.000
 XTV  CAI  CAV  OAQ  120.99  3.000
 XTV  OAB  CAR  CAJ  118.62  3.000
 XTV  OAB  CAR  CAV  122.92  3.000
 XTV  CAJ  CAR  CAV  118.47  3.000
 XTV  H5   CAJ  CAS  120.58  3.000
 XTV  H5   CAJ  CAR  118.71  3.000
 XTV  CAS  CAJ  CAR  120.71  3.000
 XTV  H6   OAB  CAR  111.08  3.000
 XTV  H7   CAI  CAH  120.46  3.000
 XTV  H7   CAI  CAV  119.74  3.000
 XTV  CAH  CAI  CAV  119.81  3.000
 XTV  H8   CAH  CAS  120.45  3.000
 XTV  H8   CAH  CAI  119.73  3.000
 XTV  CAS  CAH  CAI  119.82  3.000
 XTV  CAN  CAS  CAH  120.09  3.000
 XTV  CAN  CAS  CAJ  119.91  3.000
 XTV  CAH  CAS  CAJ  120.00  3.000
 XTV  H10  CAN  H9   107.76  3.000
 XTV  H10  CAN  NAY  106.86  3.000
 XTV  H9   CAN  NAY  108.28  3.000
 XTV  H10  CAN  CAS  111.24  3.000
 XTV  H9   CAN  CAS  111.08  3.000
 XTV  NAY  CAN  CAS  111.43  3.000
 XTV  NAP  NAY  CAK  111.15  3.000
 XTV  CAK  NAY  CAN  127.88  3.000
 XTV  NAP  NAY  CAN  120.86  3.000
 XTV  H11  CAK  CAU  132.97  3.000
 XTV  H11  CAK  NAY  122.89  3.000
 XTV  CAU  CAK  NAY  104.14  3.000
 XTV  NAO  NAP  NAY  107.82  3.000
 XTV  CAU  NAO  NAP  109.46  3.000
 XTV  CAX  CAU  NAO  122.23  3.000
 XTV  CAX  CAU  CAK  130.33  3.000
 XTV  NAO  CAU  CAK  107.44  3.000
 XTV  H12  CAX  CAM  116.56  3.000
 XTV  H12  CAX  CAL  116.55  3.000
 XTV  CAM  CAX  CAL   59.47  3.000
 XTV  H12  CAX  CAU  113.47  3.000
 XTV  CAL  CAX  CAU  120.27  3.000
 XTV  CAM  CAX  CAU  120.36  3.000
 XTV  H14  CAL  H13  114.42  3.000
 XTV  H14  CAL  CAM  118.47  3.000
 XTV  H13  CAL  CAM  118.21  3.000
 XTV  H14  CAL  CAX  117.66  3.000
 XTV  H13  CAL  CAX  117.36  3.000
 XTV  CAM  CAL  CAX   60.23  3.000
 XTV  H16  CAM  H15  114.32  3.000
 XTV  H16  CAM  CAL  118.33  3.000
 XTV  H15  CAM  CAL  118.42  3.000
 XTV  H16  CAM  CAX  117.58  3.000
 XTV  H15  CAM  CAX  117.49  3.000
 XTV  CAL  CAM  CAX   60.31  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 XTV  CONST_01  CAE  CAG  CAW  CAT     0.00   0.0  0
 XTV  CONST_02  CAE  CAD  CAF  CAT     0.00   0.0  0
 XTV  CONST_03  CAG  CAE  CAD  CAF     0.00   0.0  0
 XTV  CONST_04  CAG  CAW  CAT  CAF     0.00   0.0  0
 XTV  CONST_05  CAW  CAG  CAE  CAD     0.00   0.0  0
 XTV  CONST_06  CAW  CAT  CAF  CAD     0.00   0.0  0
 XTV  CONST_07  CAS  CAH  CAI  CAV     0.00   0.0  0
 XTV  CONST_08  CAS  CAJ  CAR  CAV     0.00   0.0  0
 XTV  CONST_09  CAH  CAI  CAV  CAR     0.00   0.0  0
 XTV  CONST_10  CAH  CAS  CAJ  CAR     0.00   0.0  0
 XTV  CONST_11  CAI  CAH  CAS  CAJ     0.00   0.0  0
 XTV  CONST_12  CAI  CAV  CAR  CAJ     0.00   0.0  0
 XTV  CONST_13  CAU  NAO  NAP  NAY     0.00   0.0  0
 XTV  CONST_14  NAO  CAU  CAK  NAY     0.00   0.0  0
 XTV  CONST_15  NAP  NAO  CAU  CAK     0.00   0.0  0
 XTV  CONST_16  NAO  NAP  NAY  CAK     0.00   0.0  0
 XTV  CONST_17  CAU  CAK  NAY  NAP     0.00   0.0  0
 XTV  CONST_18  CAX  CAU  CAK  NAY   180.00   0.0  0
 XTV  CONST_19  CAX  CAU  NAO  NAP   180.00   0.0  0
 XTV  CONST_20  CAG  CAW  CAT  CAC   180.00   0.0  0
 XTV  CONST_21  CAD  CAF  CAT  CAC   180.00   0.0  0
 XTV  CONST_22  OAQ  CAW  CAT  CAF   180.00   0.0  0
 XTV  CONST_23  OAQ  CAW  CAG  CAE   180.00   0.0  0
 XTV  CONST_24  CAH  CAI  CAV  OAQ   180.00   0.0  0
 XTV  CONST_25  CAJ  CAR  CAV  OAQ   180.00   0.0  0
 XTV  CONST_26  CAN  CAS  CAJ  CAR   180.00   0.0  0
 XTV  CONST_27  CAI  CAV  CAR  OAB   180.00   0.0  0
 XTV  CONST_28  CAS  CAJ  CAR  OAB   180.00   0.0  0
 XTV  CONST_29  CAN  CAS  CAH  CAI   180.00   0.0  0
 XTV  CONST_30  NAO  NAP  NAY  CAN   180.00   0.0  0
 XTV  CONST_31  CAU  CAK  NAY  CAN   180.00   0.0  0
 XTV  CONST_32  H4   CAG  CAW  CAT   180.00   0.0  0
 XTV  CONST_33  H2   CAD  CAF  CAT   180.00   0.0  0
 XTV  CONST_34  H3   CAE  CAD  CAF   180.00   0.0  0
 XTV  CONST_35  H1   CAF  CAD  CAE   180.00   0.0  0
 XTV  CONST_36  H8   CAH  CAI  CAV   180.00   0.0  0
 XTV  CONST_37  H5   CAJ  CAR  CAV   180.00   0.0  0
 XTV  CONST_38  H7   CAI  CAV  CAR   180.00   0.0  0
 XTV  CONST_39  H11  CAK  NAY  NAP   180.00   0.0  0
 XTV  Var_01    CAM  CAX  CAU  CAK   -32.71  30.0  1
 XTV  Var_02    CAL  CAM  CAX  CAU   109.43  30.0  1
 XTV  Var_03    CAI  CAV  OAQ  CAW   -75.29  30.0  2
 XTV  Var_04    NAY  CAN  CAS  CAJ  -109.35  30.0  2
 XTV  Var_05    NAP  NAY  CAN  CAS  -100.23  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 XTV  chir_01  CAX  CAM  CAU  CAL  both

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 XTV  plan-1  CAN  0.020
 XTV  plan-1  NAY  0.020
 XTV  plan-1  CAK  0.020
 XTV  plan-1  NAP  0.020
 XTV  plan-1  NAO  0.020
 XTV  plan-1  CAU  0.020
 XTV  plan-1  CAX  0.020
 XTV  plan-1  H11  0.020
 XTV  plan-2  NAA  0.020
 XTV  plan-2  CAC  0.020
 XTV  plan-2  CAT  0.020
 XTV  plan-2  CAF  0.020
 XTV  plan-2  CAD  0.020
 XTV  plan-2  CAE  0.020
 XTV  plan-2  CAG  0.020
 XTV  plan-2  CAW  0.020
 XTV  plan-2  OAQ  0.020
 XTV  plan-2  H1   0.020
 XTV  plan-2  H2   0.020
 XTV  plan-2  H3   0.020
 XTV  plan-2  H4   0.020
 XTV  plan-3  OAQ  0.020
 XTV  plan-3  CAV  0.020
 XTV  plan-3  CAR  0.020
 XTV  plan-3  CAJ  0.020
 XTV  plan-3  OAB  0.020
 XTV  plan-3  CAI  0.020
 XTV  plan-3  CAH  0.020
 XTV  plan-3  CAS  0.020
 XTV  plan-3  CAN  0.020
 XTV  plan-3  H5   0.020
 XTV  plan-3  H7   0.020
 XTV  plan-3  H8   0.020

